Starting phenix.real_space_refine on Fri Aug 22 17:56:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8il3_35526/08_2025/8il3_35526.cif Found real_map, /net/cci-nas-00/data/ceres_data/8il3_35526/08_2025/8il3_35526.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8il3_35526/08_2025/8il3_35526.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8il3_35526/08_2025/8il3_35526.map" model { file = "/net/cci-nas-00/data/ceres_data/8il3_35526/08_2025/8il3_35526.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8il3_35526/08_2025/8il3_35526.cif" } resolution = 3.86 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1762 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 24 5.16 5 C 3255 2.51 5 N 888 2.21 5 O 1005 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5172 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1682 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 204} Chain: "B" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1609 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 13, 'TRANS': 201} Chain: "C" Number of atoms: 1881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1881 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Time building chain proxies: 1.35, per 1000 atoms: 0.26 Number of scatterers: 5172 At special positions: 0 Unit cell: (68, 73.95, 128.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 24 16.00 O 1005 8.00 N 888 7.00 C 3255 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 44 " - pdb=" SG CYS C 59 " distance=2.97 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.33 Conformation dependent library (CDL) restraints added in 232.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1246 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 18 sheets defined 17.9% alpha, 19.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 125 through 131 Processing helix chain 'A' and resid 186 through 191 Processing helix chain 'B' and resid 87 through 91 removed outlier: 4.134A pdb=" N THR B 91 " --> pdb=" O ALA B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 197 removed outlier: 3.518A pdb=" N GLY B 195 " --> pdb=" O SER B 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 51 Processing helix chain 'C' and resid 58 through 71 removed outlier: 3.679A pdb=" N PHE C 70 " --> pdb=" O PHE C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 78 removed outlier: 3.957A pdb=" N ILE C 78 " --> pdb=" O PRO C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 89 Processing helix chain 'C' and resid 106 through 116 Processing helix chain 'C' and resid 125 through 131 Processing helix chain 'C' and resid 160 through 176 Processing helix chain 'C' and resid 198 through 203 Processing helix chain 'C' and resid 233 through 241 Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 13 removed outlier: 5.905A pdb=" N LEU A 11 " --> pdb=" O GLU A 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 20 removed outlier: 3.611A pdb=" N PHE A 75 " --> pdb=" O CYS A 23 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 19 through 20 Processing sheet with id=AA4, first strand: chain 'A' and resid 30 through 31 Processing sheet with id=AA5, first strand: chain 'A' and resid 49 through 50 Processing sheet with id=AA6, first strand: chain 'A' and resid 134 through 135 removed outlier: 3.619A pdb=" N ALA A 134 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU A 185 " --> pdb=" O ALA A 134 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 152 through 154 removed outlier: 3.543A pdb=" N LYS A 211 " --> pdb=" O CYS A 198 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 166 through 167 Processing sheet with id=AA9, first strand: chain 'B' and resid 3 through 4 Processing sheet with id=AB1, first strand: chain 'B' and resid 10 through 12 Processing sheet with id=AB2, first strand: chain 'B' and resid 10 through 12 Processing sheet with id=AB3, first strand: chain 'B' and resid 20 through 21 Processing sheet with id=AB4, first strand: chain 'B' and resid 49 through 50 Processing sheet with id=AB5, first strand: chain 'B' and resid 128 through 129 removed outlier: 3.672A pdb=" N LEU B 143 " --> pdb=" O VAL B 187 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER B 185 " --> pdb=" O CYS B 145 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N TYR B 181 " --> pdb=" O ASP B 149 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 128 through 129 removed outlier: 3.672A pdb=" N LEU B 143 " --> pdb=" O VAL B 187 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER B 185 " --> pdb=" O CYS B 145 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N TYR B 181 " --> pdb=" O ASP B 149 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 201 through 202 Processing sheet with id=AB8, first strand: chain 'C' and resid 179 through 181 removed outlier: 8.203A pdb=" N ASP C 179 " --> pdb=" O GLN C 213 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N LEU C 215 " --> pdb=" O ASP C 179 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL C 181 " --> pdb=" O LEU C 215 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 184 through 185 removed outlier: 6.862A pdb=" N VAL C 219 " --> pdb=" O ILE C 255 " (cutoff:3.500A) 145 hydrogen bonds defined for protein. 357 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.80 Time building geometry restraints manager: 0.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1301 1.33 - 1.45: 1179 1.45 - 1.58: 2788 1.58 - 1.70: 0 1.70 - 1.82: 29 Bond restraints: 5297 Sorted by residual: bond pdb=" N VAL B 189 " pdb=" CA VAL B 189 " ideal model delta sigma weight residual 1.461 1.493 -0.033 8.70e-03 1.32e+04 1.40e+01 bond pdb=" N ILE C 105 " pdb=" CA ILE C 105 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.22e-02 6.72e+03 1.08e+01 bond pdb=" N CYS C 157 " pdb=" CA CYS C 157 " ideal model delta sigma weight residual 1.455 1.495 -0.040 1.23e-02 6.61e+03 1.04e+01 bond pdb=" N CYS C 231 " pdb=" CA CYS C 231 " ideal model delta sigma weight residual 1.456 1.496 -0.040 1.23e-02 6.61e+03 1.04e+01 bond pdb=" N ASP C 152 " pdb=" CA ASP C 152 " ideal model delta sigma weight residual 1.453 1.495 -0.042 1.31e-02 5.83e+03 1.01e+01 ... (remaining 5292 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 6474 2.15 - 4.30: 604 4.30 - 6.45: 100 6.45 - 8.60: 16 8.60 - 10.75: 6 Bond angle restraints: 7200 Sorted by residual: angle pdb=" N PRO A 145 " pdb=" CA PRO A 145 " pdb=" C PRO A 145 " ideal model delta sigma weight residual 112.26 101.75 10.51 1.44e+00 4.82e-01 5.33e+01 angle pdb=" N VAL C 45 " pdb=" CA VAL C 45 " pdb=" C VAL C 45 " ideal model delta sigma weight residual 110.72 104.26 6.46 1.01e+00 9.80e-01 4.09e+01 angle pdb=" N PHE A 143 " pdb=" CA PHE A 143 " pdb=" C PHE A 143 " ideal model delta sigma weight residual 113.97 120.31 -6.34 1.28e+00 6.10e-01 2.45e+01 angle pdb=" N ASP C 229 " pdb=" CA ASP C 229 " pdb=" C ASP C 229 " ideal model delta sigma weight residual 111.56 104.50 7.06 1.43e+00 4.89e-01 2.44e+01 angle pdb=" N GLN C 84 " pdb=" CA GLN C 84 " pdb=" C GLN C 84 " ideal model delta sigma weight residual 109.81 120.33 -10.52 2.21e+00 2.05e-01 2.27e+01 ... (remaining 7195 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 2701 17.97 - 35.95: 336 35.95 - 53.92: 96 53.92 - 71.89: 27 71.89 - 89.87: 8 Dihedral angle restraints: 3168 sinusoidal: 1236 harmonic: 1932 Sorted by residual: dihedral pdb=" CB CYS C 44 " pdb=" SG CYS C 44 " pdb=" SG CYS C 59 " pdb=" CB CYS C 59 " ideal model delta sinusoidal sigma weight residual 93.00 -179.04 -87.96 1 1.00e+01 1.00e-02 9.26e+01 dihedral pdb=" CA THR B 101 " pdb=" C THR B 101 " pdb=" N PRO B 102 " pdb=" CA PRO B 102 " ideal model delta harmonic sigma weight residual 180.00 153.19 26.81 0 5.00e+00 4.00e-02 2.87e+01 dihedral pdb=" CA MET C 54 " pdb=" C MET C 54 " pdb=" N ARG C 55 " pdb=" CA ARG C 55 " ideal model delta harmonic sigma weight residual 180.00 153.47 26.53 0 5.00e+00 4.00e-02 2.82e+01 ... (remaining 3165 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 505 0.061 - 0.121: 177 0.121 - 0.182: 78 0.182 - 0.242: 31 0.242 - 0.303: 9 Chirality restraints: 800 Sorted by residual: chirality pdb=" CA GLN C 84 " pdb=" N GLN C 84 " pdb=" C GLN C 84 " pdb=" CB GLN C 84 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CA CYS C 44 " pdb=" N CYS C 44 " pdb=" C CYS C 44 " pdb=" CB CYS C 44 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" CB VAL C 202 " pdb=" CA VAL C 202 " pdb=" CG1 VAL C 202 " pdb=" CG2 VAL C 202 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.94e+00 ... (remaining 797 not shown) Planarity restraints: 928 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 105 " -0.053 5.00e-02 4.00e+02 7.97e-02 1.02e+01 pdb=" N PRO B 106 " 0.138 5.00e-02 4.00e+02 pdb=" CA PRO B 106 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 106 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 101 " -0.052 5.00e-02 4.00e+02 7.80e-02 9.73e+00 pdb=" N PRO B 102 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO B 102 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 102 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 199 " 0.015 2.00e-02 2.50e+03 3.07e-02 9.44e+00 pdb=" C PHE C 199 " -0.053 2.00e-02 2.50e+03 pdb=" O PHE C 199 " 0.020 2.00e-02 2.50e+03 pdb=" N GLY C 200 " 0.018 2.00e-02 2.50e+03 ... (remaining 925 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 1859 2.87 - 3.38: 4397 3.38 - 3.88: 8911 3.88 - 4.39: 9170 4.39 - 4.90: 15848 Nonbonded interactions: 40185 Sorted by model distance: nonbonded pdb=" O GLU C 238 " pdb=" OG SER C 241 " model vdw 2.362 3.040 nonbonded pdb=" O ARG C 35 " pdb=" OG1 THR C 39 " model vdw 2.366 3.040 nonbonded pdb=" O THR A 87 " pdb=" OG1 THR A 87 " model vdw 2.370 3.040 nonbonded pdb=" O GLU A 127 " pdb=" OG SER A 131 " model vdw 2.374 3.040 nonbonded pdb=" OG SER C 227 " pdb=" OD1 ASP C 233 " model vdw 2.388 3.040 ... (remaining 40180 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.510 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.936 5298 Z= 0.846 Angle : 1.433 23.461 7202 Z= 0.893 Chirality : 0.084 0.303 800 Planarity : 0.010 0.080 928 Dihedral : 18.377 89.866 1919 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.62 % Favored : 89.38 % Rotamer: Outliers : 8.75 % Allowed : 16.47 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.16 (0.25), residues: 659 helix: -3.96 (0.24), residues: 116 sheet: -3.82 (0.32), residues: 167 loop : -3.10 (0.25), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 54 TYR 0.020 0.003 TYR B 107 PHE 0.038 0.004 PHE C 112 TRP 0.019 0.003 TRP B 108 HIS 0.011 0.002 HIS B 35 Details of bonding type rmsd covalent geometry : bond 0.00932 ( 5297) covalent geometry : angle 1.38594 ( 7200) SS BOND : bond 0.93563 ( 1) SS BOND : angle 21.92595 ( 2) hydrogen bonds : bond 0.26248 ( 127) hydrogen bonds : angle 9.80119 ( 357) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 55 time to evaluate : 0.164 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 LEU cc_start: 0.8660 (mt) cc_final: 0.8375 (mp) REVERT: A 112 ARG cc_start: 0.5701 (OUTLIER) cc_final: 0.4337 (ppt170) REVERT: A 174 ASP cc_start: 0.6356 (p0) cc_final: 0.5614 (p0) REVERT: B 31 ASP cc_start: 0.8401 (t0) cc_final: 0.8020 (t70) REVERT: B 187 VAL cc_start: 0.7476 (OUTLIER) cc_final: 0.7253 (m) REVERT: B 197 GLN cc_start: 0.2839 (OUTLIER) cc_final: 0.2554 (tm-30) REVERT: C 92 GLN cc_start: 0.7180 (tt0) cc_final: 0.6980 (tt0) outliers start: 51 outliers final: 17 residues processed: 102 average time/residue: 0.0888 time to fit residues: 11.2248 Evaluate side-chains 50 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 30 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 CYS Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 169 HIS Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain C residue 59 CYS Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 162 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 8.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 64 optimal weight: 0.0570 overall best weight: 0.8700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN A 214 ASN B 176 GLN C 25 GLN C 116 GLN ** C 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.100085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.085402 restraints weight = 18846.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.087339 restraints weight = 12461.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.088669 restraints weight = 9226.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.089672 restraints weight = 7403.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.090359 restraints weight = 6251.531| |-----------------------------------------------------------------------------| r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 5298 Z= 0.140 Angle : 0.681 7.990 7202 Z= 0.356 Chirality : 0.043 0.134 800 Planarity : 0.006 0.057 928 Dihedral : 9.006 81.421 743 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 5.32 % Allowed : 19.21 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.19 (0.27), residues: 659 helix: -2.16 (0.38), residues: 120 sheet: -3.38 (0.32), residues: 178 loop : -2.69 (0.28), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 228 TYR 0.020 0.002 TYR A 144 PHE 0.010 0.001 PHE C 66 TRP 0.008 0.001 TRP C 136 HIS 0.003 0.001 HIS B 59 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 5297) covalent geometry : angle 0.68052 ( 7200) SS BOND : bond 0.00628 ( 1) SS BOND : angle 1.80165 ( 2) hydrogen bonds : bond 0.04989 ( 127) hydrogen bonds : angle 6.72009 ( 357) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 37 time to evaluate : 0.134 Fit side-chains REVERT: A 112 ARG cc_start: 0.5902 (OUTLIER) cc_final: 0.4335 (ppt170) REVERT: A 174 ASP cc_start: 0.6355 (p0) cc_final: 0.5837 (p0) REVERT: A 179 LEU cc_start: 0.9285 (tp) cc_final: 0.8408 (mp) REVERT: B 31 ASP cc_start: 0.8103 (t0) cc_final: 0.7792 (t70) REVERT: C 25 GLN cc_start: 0.6346 (OUTLIER) cc_final: 0.5811 (tm-30) REVERT: C 97 ASN cc_start: 0.7705 (m-40) cc_final: 0.7281 (m-40) outliers start: 31 outliers final: 16 residues processed: 66 average time/residue: 0.0641 time to fit residues: 5.6723 Evaluate side-chains 47 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 29 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 CYS Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 150 TYR Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 169 HIS Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain C residue 25 GLN Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 162 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 21 optimal weight: 10.0000 chunk 48 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 53 optimal weight: 5.9990 chunk 25 optimal weight: 0.5980 chunk 45 optimal weight: 0.0570 chunk 31 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 51 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.100470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.085870 restraints weight = 18664.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.087742 restraints weight = 12435.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.089081 restraints weight = 9276.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.090043 restraints weight = 7463.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.090748 restraints weight = 6306.385| |-----------------------------------------------------------------------------| r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 5298 Z= 0.108 Angle : 0.606 6.331 7202 Z= 0.310 Chirality : 0.041 0.124 800 Planarity : 0.005 0.048 928 Dihedral : 6.752 59.553 725 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 4.12 % Allowed : 21.27 % Favored : 74.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.55 (0.29), residues: 659 helix: -1.17 (0.44), residues: 119 sheet: -3.03 (0.33), residues: 178 loop : -2.41 (0.29), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 38 TYR 0.017 0.002 TYR A 144 PHE 0.013 0.001 PHE A 75 TRP 0.008 0.001 TRP B 108 HIS 0.006 0.001 HIS C 74 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 5297) covalent geometry : angle 0.60555 ( 7200) SS BOND : bond 0.00341 ( 1) SS BOND : angle 1.12750 ( 2) hydrogen bonds : bond 0.03795 ( 127) hydrogen bonds : angle 6.17002 ( 357) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 33 time to evaluate : 0.186 Fit side-chains REVERT: A 112 ARG cc_start: 0.5963 (OUTLIER) cc_final: 0.4297 (ppt170) REVERT: A 174 ASP cc_start: 0.6072 (p0) cc_final: 0.5567 (p0) REVERT: A 179 LEU cc_start: 0.9179 (tp) cc_final: 0.8438 (mp) REVERT: B 31 ASP cc_start: 0.8068 (t0) cc_final: 0.7761 (t70) outliers start: 24 outliers final: 18 residues processed: 55 average time/residue: 0.0759 time to fit residues: 5.5328 Evaluate side-chains 47 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 28 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 CYS Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 150 TYR Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 169 HIS Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 162 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 52 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 44 optimal weight: 0.2980 chunk 37 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 23 optimal weight: 8.9990 chunk 12 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 GLN ** A 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 35 HIS B 59 HIS ** B 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 51 HIS C 56 HIS C 146 ASN ** C 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.094454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.080379 restraints weight = 19162.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.082117 restraints weight = 12882.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.083362 restraints weight = 9684.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.084253 restraints weight = 7838.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.084901 restraints weight = 6671.945| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 5298 Z= 0.235 Angle : 0.746 7.116 7202 Z= 0.389 Chirality : 0.045 0.153 800 Planarity : 0.005 0.051 928 Dihedral : 7.181 49.692 723 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.41 % Favored : 90.59 % Rotamer: Outliers : 6.00 % Allowed : 21.78 % Favored : 72.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.51 (0.30), residues: 659 helix: -1.09 (0.44), residues: 111 sheet: -3.11 (0.32), residues: 199 loop : -2.21 (0.31), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 54 TYR 0.029 0.002 TYR A 144 PHE 0.027 0.003 PHE C 66 TRP 0.011 0.002 TRP A 39 HIS 0.005 0.001 HIS B 59 Details of bonding type rmsd covalent geometry : bond 0.00541 ( 5297) covalent geometry : angle 0.74571 ( 7200) SS BOND : bond 0.00617 ( 1) SS BOND : angle 1.79669 ( 2) hydrogen bonds : bond 0.05719 ( 127) hydrogen bonds : angle 6.70365 ( 357) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 30 time to evaluate : 0.216 Fit side-chains REVERT: A 112 ARG cc_start: 0.6484 (OUTLIER) cc_final: 0.4686 (ppt170) REVERT: A 174 ASP cc_start: 0.6136 (p0) cc_final: 0.5604 (p0) REVERT: B 31 ASP cc_start: 0.8054 (t0) cc_final: 0.7728 (t70) outliers start: 35 outliers final: 25 residues processed: 62 average time/residue: 0.0741 time to fit residues: 6.1061 Evaluate side-chains 53 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 27 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 150 TYR Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 169 HIS Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain C residue 59 CYS Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 212 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 35 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 28 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 63 optimal weight: 0.0670 chunk 3 optimal weight: 0.7980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 51 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.097318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.082728 restraints weight = 18778.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.084595 restraints weight = 12448.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.085923 restraints weight = 9259.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.086844 restraints weight = 7454.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.087499 restraints weight = 6341.229| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5298 Z= 0.113 Angle : 0.612 6.924 7202 Z= 0.310 Chirality : 0.042 0.123 800 Planarity : 0.004 0.046 928 Dihedral : 6.239 51.556 722 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 3.95 % Allowed : 24.53 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.10 (0.30), residues: 659 helix: -0.75 (0.46), residues: 117 sheet: -2.77 (0.33), residues: 181 loop : -2.10 (0.31), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 104 TYR 0.016 0.001 TYR A 53 PHE 0.010 0.001 PHE B 95 TRP 0.007 0.001 TRP C 27 HIS 0.003 0.001 HIS B 35 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 5297) covalent geometry : angle 0.61204 ( 7200) SS BOND : bond 0.00329 ( 1) SS BOND : angle 1.05342 ( 2) hydrogen bonds : bond 0.03905 ( 127) hydrogen bonds : angle 6.07306 ( 357) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 29 time to evaluate : 0.223 Fit side-chains revert: symmetry clash REVERT: A 112 ARG cc_start: 0.6344 (OUTLIER) cc_final: 0.4506 (ppt170) REVERT: A 174 ASP cc_start: 0.5914 (p0) cc_final: 0.5486 (p0) REVERT: B 31 ASP cc_start: 0.8040 (t0) cc_final: 0.7744 (t70) REVERT: B 110 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.7866 (pt0) REVERT: B 181 TYR cc_start: 0.7368 (m-80) cc_final: 0.7069 (m-10) outliers start: 23 outliers final: 17 residues processed: 51 average time/residue: 0.0886 time to fit residues: 5.9306 Evaluate side-chains 46 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 27 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 110 GLN Chi-restraints excluded: chain B residue 150 TYR Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 169 HIS Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 162 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 37 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 13 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 23 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 42 optimal weight: 0.0030 chunk 50 optimal weight: 0.7980 overall best weight: 1.0994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.097013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.082482 restraints weight = 19384.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.084350 restraints weight = 12902.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.085658 restraints weight = 9608.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.086622 restraints weight = 7712.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.087234 restraints weight = 6523.181| |-----------------------------------------------------------------------------| r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.3468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5298 Z= 0.130 Angle : 0.607 6.584 7202 Z= 0.307 Chirality : 0.042 0.125 800 Planarity : 0.004 0.043 928 Dihedral : 6.008 51.649 722 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 4.63 % Allowed : 24.01 % Favored : 71.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.85 (0.31), residues: 659 helix: -0.56 (0.46), residues: 117 sheet: -2.70 (0.36), residues: 159 loop : -1.97 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 54 TYR 0.014 0.001 TYR A 144 PHE 0.012 0.001 PHE C 66 TRP 0.006 0.001 TRP A 39 HIS 0.003 0.001 HIS B 35 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 5297) covalent geometry : angle 0.60666 ( 7200) SS BOND : bond 0.00417 ( 1) SS BOND : angle 1.02414 ( 2) hydrogen bonds : bond 0.04001 ( 127) hydrogen bonds : angle 5.92850 ( 357) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 31 time to evaluate : 0.221 Fit side-chains revert: symmetry clash REVERT: A 112 ARG cc_start: 0.6378 (OUTLIER) cc_final: 0.4498 (ppt170) REVERT: A 174 ASP cc_start: 0.6009 (p0) cc_final: 0.5582 (p0) REVERT: B 31 ASP cc_start: 0.8020 (t0) cc_final: 0.7718 (t70) REVERT: B 110 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.7937 (pt0) REVERT: B 181 TYR cc_start: 0.7399 (m-80) cc_final: 0.6984 (m-80) REVERT: C 47 TYR cc_start: 0.8085 (t80) cc_final: 0.7878 (t80) outliers start: 27 outliers final: 21 residues processed: 56 average time/residue: 0.0734 time to fit residues: 5.5201 Evaluate side-chains 48 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 25 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 110 GLN Chi-restraints excluded: chain B residue 150 TYR Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 146 ASN Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 162 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 62 optimal weight: 7.9990 chunk 35 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 chunk 36 optimal weight: 0.0050 chunk 53 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 11 optimal weight: 0.1980 chunk 24 optimal weight: 2.9990 chunk 59 optimal weight: 8.9990 chunk 38 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.098118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.083647 restraints weight = 18604.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.085538 restraints weight = 12327.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.086842 restraints weight = 9140.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.087820 restraints weight = 7366.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.088536 restraints weight = 6201.861| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 5298 Z= 0.099 Angle : 0.574 7.214 7202 Z= 0.288 Chirality : 0.041 0.123 800 Planarity : 0.004 0.040 928 Dihedral : 5.537 54.064 720 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 4.46 % Allowed : 25.39 % Favored : 70.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.67 (0.31), residues: 659 helix: -0.28 (0.47), residues: 118 sheet: -2.68 (0.36), residues: 161 loop : -1.84 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 55 TYR 0.017 0.001 TYR A 53 PHE 0.011 0.001 PHE A 75 TRP 0.006 0.001 TRP C 27 HIS 0.003 0.001 HIS B 35 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 5297) covalent geometry : angle 0.57361 ( 7200) SS BOND : bond 0.00312 ( 1) SS BOND : angle 0.68955 ( 2) hydrogen bonds : bond 0.03453 ( 127) hydrogen bonds : angle 5.68678 ( 357) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 29 time to evaluate : 0.229 Fit side-chains revert: symmetry clash REVERT: B 31 ASP cc_start: 0.8015 (t0) cc_final: 0.7640 (t70) REVERT: B 181 TYR cc_start: 0.7230 (m-80) cc_final: 0.6918 (m-10) REVERT: C 135 THR cc_start: 0.8003 (OUTLIER) cc_final: 0.7691 (p) outliers start: 26 outliers final: 20 residues processed: 52 average time/residue: 0.0733 time to fit residues: 5.1230 Evaluate side-chains 46 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 25 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 150 TYR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 146 ASN Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 162 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 33 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.097593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.083295 restraints weight = 19005.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.085157 restraints weight = 12548.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.086485 restraints weight = 9317.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.087440 restraints weight = 7471.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.088038 restraints weight = 6308.167| |-----------------------------------------------------------------------------| r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5298 Z= 0.114 Angle : 0.576 7.309 7202 Z= 0.289 Chirality : 0.041 0.122 800 Planarity : 0.004 0.040 928 Dihedral : 5.023 34.204 716 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 4.12 % Allowed : 26.42 % Favored : 69.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.56 (0.32), residues: 659 helix: -0.21 (0.47), residues: 118 sheet: -2.56 (0.37), residues: 161 loop : -1.79 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 104 TYR 0.011 0.001 TYR A 144 PHE 0.010 0.001 PHE C 66 TRP 0.005 0.001 TRP A 39 HIS 0.003 0.001 HIS B 35 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 5297) covalent geometry : angle 0.57597 ( 7200) SS BOND : bond 0.00403 ( 1) SS BOND : angle 0.87755 ( 2) hydrogen bonds : bond 0.03641 ( 127) hydrogen bonds : angle 5.68394 ( 357) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 29 time to evaluate : 0.217 Fit side-chains revert: symmetry clash REVERT: B 31 ASP cc_start: 0.7916 (t0) cc_final: 0.7616 (t70) outliers start: 24 outliers final: 23 residues processed: 51 average time/residue: 0.0736 time to fit residues: 5.1694 Evaluate side-chains 47 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 24 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 CYS Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 150 TYR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 146 ASN Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 162 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 6 optimal weight: 0.0020 chunk 39 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 chunk 13 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.1792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.095993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.081519 restraints weight = 18866.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.083441 restraints weight = 12696.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.084750 restraints weight = 9402.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.085674 restraints weight = 7520.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.086389 restraints weight = 6377.165| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5298 Z= 0.132 Angle : 0.599 7.656 7202 Z= 0.302 Chirality : 0.041 0.128 800 Planarity : 0.004 0.044 928 Dihedral : 5.182 35.240 716 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 4.97 % Allowed : 25.04 % Favored : 69.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.47 (0.32), residues: 659 helix: -0.25 (0.46), residues: 118 sheet: -2.36 (0.38), residues: 163 loop : -1.76 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 72 TYR 0.013 0.001 TYR A 144 PHE 0.012 0.001 PHE B 95 TRP 0.009 0.001 TRP A 39 HIS 0.003 0.001 HIS B 35 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 5297) covalent geometry : angle 0.59932 ( 7200) SS BOND : bond 0.00455 ( 1) SS BOND : angle 0.98532 ( 2) hydrogen bonds : bond 0.03909 ( 127) hydrogen bonds : angle 5.79586 ( 357) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 27 time to evaluate : 0.224 Fit side-chains revert: symmetry clash REVERT: B 31 ASP cc_start: 0.7902 (t0) cc_final: 0.7591 (t70) REVERT: C 100 LEU cc_start: 0.7552 (tt) cc_final: 0.7205 (tt) outliers start: 29 outliers final: 23 residues processed: 53 average time/residue: 0.0680 time to fit residues: 5.0403 Evaluate side-chains 49 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 26 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 150 TYR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 162 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 44 optimal weight: 0.0870 chunk 55 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 42 optimal weight: 7.9990 chunk 59 optimal weight: 8.9990 chunk 62 optimal weight: 0.0570 chunk 23 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.097507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.083254 restraints weight = 19154.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.085031 restraints weight = 12704.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.086353 restraints weight = 9464.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.087296 restraints weight = 7567.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.087916 restraints weight = 6389.951| |-----------------------------------------------------------------------------| r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.3953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 5298 Z= 0.099 Angle : 0.573 8.450 7202 Z= 0.285 Chirality : 0.041 0.124 800 Planarity : 0.004 0.041 928 Dihedral : 4.876 32.518 716 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 3.95 % Allowed : 26.24 % Favored : 69.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.34 (0.32), residues: 659 helix: -0.00 (0.48), residues: 118 sheet: -2.33 (0.38), residues: 161 loop : -1.70 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 72 TYR 0.008 0.001 TYR A 144 PHE 0.017 0.001 PHE C 70 TRP 0.008 0.001 TRP C 102 HIS 0.004 0.001 HIS C 51 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 5297) covalent geometry : angle 0.57350 ( 7200) SS BOND : bond 0.00307 ( 1) SS BOND : angle 0.38726 ( 2) hydrogen bonds : bond 0.03377 ( 127) hydrogen bonds : angle 5.53472 ( 357) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 29 time to evaluate : 0.220 Fit side-chains revert: symmetry clash REVERT: B 31 ASP cc_start: 0.7874 (t0) cc_final: 0.7587 (t70) REVERT: C 100 LEU cc_start: 0.7538 (tt) cc_final: 0.7167 (tt) outliers start: 23 outliers final: 22 residues processed: 49 average time/residue: 0.0661 time to fit residues: 4.5230 Evaluate side-chains 49 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 27 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 150 TYR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 146 ASN Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 162 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 45 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 chunk 61 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 32 optimal weight: 8.9990 chunk 54 optimal weight: 0.0470 chunk 2 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 overall best weight: 0.9484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN ** C 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.096674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.082740 restraints weight = 19194.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.084513 restraints weight = 12765.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.085783 restraints weight = 9484.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.086698 restraints weight = 7599.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.087383 restraints weight = 6407.485| |-----------------------------------------------------------------------------| r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5298 Z= 0.115 Angle : 0.586 8.242 7202 Z= 0.291 Chirality : 0.041 0.122 800 Planarity : 0.004 0.044 928 Dihedral : 4.927 32.939 716 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 3.77 % Allowed : 26.42 % Favored : 69.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.29 (0.32), residues: 659 helix: -0.00 (0.47), residues: 117 sheet: -2.10 (0.38), residues: 156 loop : -1.77 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 72 TYR 0.015 0.001 TYR A 53 PHE 0.018 0.001 PHE C 70 TRP 0.007 0.001 TRP C 102 HIS 0.005 0.001 HIS C 51 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 5297) covalent geometry : angle 0.58564 ( 7200) SS BOND : bond 0.00385 ( 1) SS BOND : angle 0.68858 ( 2) hydrogen bonds : bond 0.03582 ( 127) hydrogen bonds : angle 5.60144 ( 357) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1029.30 seconds wall clock time: 18 minutes 35.45 seconds (1115.45 seconds total)